[English] 日本語
Yorodumi
- PDB-5jtv: USP7CD-UBL45 in complex with Ubiquitin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jtv
TitleUSP7CD-UBL45 in complex with Ubiquitin
Components
  • Polyubiquitin-B
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / USP7 / HAUSP / C-terminal activation
Function / homology
Function and homology information


regulation of telomere capping / : / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / negative regulation of gene expression via chromosomal CpG island methylation / regulation of DNA-binding transcription factor activity / hypothalamus gonadotrophin-releasing hormone neuron development / Evasion by RSV of host interferon responses / K48-linked deubiquitinase activity ...regulation of telomere capping / : / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / negative regulation of gene expression via chromosomal CpG island methylation / regulation of DNA-binding transcription factor activity / hypothalamus gonadotrophin-releasing hormone neuron development / Evasion by RSV of host interferon responses / K48-linked deubiquitinase activity / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / symbiont-mediated disruption of host cell PML body / fat pad development / female gonad development / negative regulation of NF-kappaB transcription factor activity / seminiferous tubule development / male meiosis I / protein deubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / negative regulation of gluconeogenesis / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / negative regulation of TORC1 signaling / FLT3 signaling by CBL mutants / Signaling by ALK fusions and activated point mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / neuron projection morphogenesis / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / regulation of signal transduction by p53 class mediator / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Ubiquitin specific protease (USP) domain signature 2. ...Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.312 Å
AuthorsMurray, J.M. / Rouge, L.
CitationJournal: Structure / Year: 2016
Title: Molecular Understanding of USP7 Substrate Recognition and C-Terminal Activation.
Authors: Rouge, L. / Bainbridge, T.W. / Kwok, M. / Tong, R. / Di Lello, P. / Wertz, I.E. / Maurer, T. / Ernst, J.A. / Murray, J.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Polyubiquitin-B
C: Ubiquitin carboxyl-terminal hydrolase 7
D: Polyubiquitin-B
E: Ubiquitin carboxyl-terminal hydrolase 7
F: Polyubiquitin-B
G: Ubiquitin carboxyl-terminal hydrolase 7
H: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)310,6378
Polymers310,6378
Non-polymers00
Water0
1
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)77,6592
Polymers77,6592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-5 kcal/mol
Surface area32980 Å2
MethodPISA
2
C: Ubiquitin carboxyl-terminal hydrolase 7
D: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)77,6592
Polymers77,6592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-6 kcal/mol
Surface area32510 Å2
MethodPISA
3
E: Ubiquitin carboxyl-terminal hydrolase 7
F: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)77,6592
Polymers77,6592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-6 kcal/mol
Surface area32400 Å2
MethodPISA
4
G: Ubiquitin carboxyl-terminal hydrolase 7
H: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)77,6592
Polymers77,6592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-6 kcal/mol
Surface area32210 Å2
MethodPISA
5
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Polyubiquitin-B
E: Ubiquitin carboxyl-terminal hydrolase 7
F: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)155,3184
Polymers155,3184
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12370 Å2
ΔGint-37 kcal/mol
Surface area59890 Å2
MethodPISA
6


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28780 Å2
ΔGint-80 kcal/mol
Surface area115110 Å2
MethodPISA
7
C: Ubiquitin carboxyl-terminal hydrolase 7
D: Polyubiquitin-B
G: Ubiquitin carboxyl-terminal hydrolase 7
H: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)155,3184
Polymers155,3184
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint-39 kcal/mol
Surface area59530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.611, 115.520, 257.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Ubiquitin carboxyl-terminal hydrolase 7 / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin ...Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7


Mass: 69082.352 Da / Num. of mol.: 4
Fragment: UNP residues 193-538 LINKED via GGSGGSGGSG to Residues 866-1102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli (E. coli) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Protein
Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.273→46.954 Å / Num. obs: 52986 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 100.37 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.055 / Rrim(I) all: 0.139 / Net I/σ(I): 11.4 / Num. measured all: 323509
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.273-3.2846.30.853199.6
15.182-115.4550.036198.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXdev_2210refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1nbf

1nbf


Resolution: 3.312→46.954 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 2594 5.09 %
Rwork0.2386 --
obs0.2402 50930 99.37 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.312→46.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20520 0 0 0 20520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00420943
X-RAY DIFFRACTIONf_angle_d0.80828263
X-RAY DIFFRACTIONf_dihedral_angle_d15.49712707
X-RAY DIFFRACTIONf_chiral_restr0.0483077
X-RAY DIFFRACTIONf_plane_restr0.0053694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3124-3.37270.38661320.32122293X-RAY DIFFRACTION92
3.3727-3.43750.35581290.32292539X-RAY DIFFRACTION100
3.4375-3.50770.37941380.31732494X-RAY DIFFRACTION100
3.5077-3.58390.33441420.29822492X-RAY DIFFRACTION100
3.5839-3.66720.32941570.29782519X-RAY DIFFRACTION100
3.6672-3.75890.3681330.2972525X-RAY DIFFRACTION100
3.7589-3.86050.36271500.3022521X-RAY DIFFRACTION100
3.8605-3.9740.36571250.2772524X-RAY DIFFRACTION100
3.974-4.10220.34011460.25442529X-RAY DIFFRACTION100
4.1022-4.24880.28371310.24842536X-RAY DIFFRACTION100
4.2488-4.41880.26741340.23742543X-RAY DIFFRACTION100
4.4188-4.61970.26521320.22422583X-RAY DIFFRACTION100
4.6197-4.8630.261120.22032563X-RAY DIFFRACTION100
4.863-5.16730.23261300.21762566X-RAY DIFFRACTION100
5.1673-5.56570.27561280.23372567X-RAY DIFFRACTION100
5.5657-6.12480.26111640.25272564X-RAY DIFFRACTION100
6.1248-7.00850.30051220.25052626X-RAY DIFFRACTION100
7.0085-8.82040.22811500.21822624X-RAY DIFFRACTION100
8.8204-46.95920.18251390.18672728X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -33.298 Å / Origin y: 3.8899 Å / Origin z: 32.2674 Å
111213212223313233
T1.0941 Å20.0708 Å2-0.0968 Å2-1.1306 Å2-0.1244 Å2--1.1583 Å2
L0.423 °20.0285 °20.0674 °2-0.6102 °20.2175 °2--0.9121 °2
S-0.0635 Å °0.0714 Å °-0.001 Å °-0.0117 Å °-0.0995 Å °0.1305 Å °-0.1806 Å °-0.1951 Å °0.0001 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more